recipe bioconductor-eegc

This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic cells to primary cells based on high throughput gene expression data screened either by DNA microarray or RNA sequencing. The package takes gene expression profiles as inputs from three types of samples: (i) somatic or stem cells to be (trans)differentiated (input of the engineering process), (ii) induced cells to be evaluated (output of the engineering process) and (iii) target primary cells (reference for the output). The package performs differential gene expression analysis for each pair-wise sample comparison to identify and evaluate the transcriptional differences among the 3 types of samples (input, output, reference). The ideal goal is to have induced and primary reference cell showing overlapping profiles, both very different from the original cells.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/eegc.html

License

GPL-2

Recipe

/bioconductor-eegc/meta.yaml

package bioconductor-eegc

(downloads) docker_bioconductor-eegc

Versions

1.8.1-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-clusterprofiler

>=3.10.0,<3.11.0

Depends bioconductor-deseq2

>=1.22.0,<1.23.0

Depends bioconductor-dose

>=3.8.0,<3.9.0

Depends bioconductor-edger

>=3.24.0,<3.25.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-org.hs.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-org.mm.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-ggplot2

Depends r-gplots

Depends r-igraph

Depends r-pheatmap

Depends r-r.utils

Depends r-sna

Depends r-wordcloud

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-eegc

and update with:

conda update bioconductor-eegc

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-eegc:<tag>

(see bioconductor-eegc/tags for valid values for <tag>)